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- PDB-9zz6: The ER membrane protein complex acts as a chaperone to promote vo... -

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Basic information

Entry
Database: PDB / ID: 9zz6
TitleThe ER membrane protein complex acts as a chaperone to promote voltage-gated calcium channel assembly
Components
  • (ER membrane protein complex subunit ...) x 8
  • Membrane magnesium transporter 1
  • Nanobody E2
  • Nanobody G9
KeywordsCHAPERONE/IMMUNE SYSTEM / protein biogenesis / endoplasmic reticulum / ER / chaperone / insertase / complex / membrane protein / CHAPERONE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


extrinsic component of endoplasmic reticulum membrane / EMC complex / : / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / tail-anchored membrane protein insertion into ER membrane / Miscellaneous transport and binding events / cobalt ion transmembrane transporter activity / ferrous iron transmembrane transporter activity ...extrinsic component of endoplasmic reticulum membrane / EMC complex / : / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / tail-anchored membrane protein insertion into ER membrane / Miscellaneous transport and binding events / cobalt ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / copper ion transport / magnesium ion transmembrane transporter activity / RHOA GTPase cycle / autophagosome assembly / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / positive regulation of angiogenesis / carbohydrate binding / early endosome membrane / angiogenesis / early endosome / Golgi membrane / apoptotic process / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / protein-containing complex / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
EMC1 N-terminal beta-propeller domain / ER membrane protein complex subunit 8/9 / : / Uncharacterised protein family (UPF0172) / EMC2 TPR-like repeat domain / TMEM85/ER membrane protein complex subunit 4 / ER membrane protein complex subunit 4 / ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain ...EMC1 N-terminal beta-propeller domain / ER membrane protein complex subunit 8/9 / : / Uncharacterised protein family (UPF0172) / EMC2 TPR-like repeat domain / TMEM85/ER membrane protein complex subunit 4 / ER membrane protein complex subunit 4 / ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 6 / ER membrane protein complex subunit 3 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 1 / ER membrane protein complex subunit 6-like / EMC6 / ER membrane protein complex subunit 1, second beta-propeller / Membrane magnesium transporter / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 2-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein DUF106 / Carbohydrate-binding-like fold / Quinoprotein alcohol dehydrogenase-like superfamily / TPR repeat region circular profile. / TPR repeat profile. / MPN domain / MPN domain profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
ER membrane protein complex subunit 8 / ER membrane protein complex subunit 2 / ER membrane protein complex subunit 4 / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 5 / ER membrane protein complex subunit 1 / ER membrane protein complex subunit 6 / Endoplasmic reticulum membrane protein complex subunit 7 / ER membrane protein complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.16 Å
AuthorsSingal, B. / Biswal, M. / Pleiner, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: bioRxiv / Year: 2026
Title: The ER membrane protein complex acts as a chaperone to promote the biogenesis of multi-bundle membrane proteins.
Authors: Marinda Stanton / Bharti Singal / Mahamaya Biswal / Megha Agarwal / Caroline Elizabeth Scheuing / Gerardo Dasaev Vargas / Alex Gao / Casey A Gifford / Tino Pleiner /
Abstract: Nearly half of the ~5,000 human membrane proteins need to assemble into stoichiometric complexes as part of their biogenesis at the endoplasmic reticulum (ER) membrane. How ER resident biogenesis ...Nearly half of the ~5,000 human membrane proteins need to assemble into stoichiometric complexes as part of their biogenesis at the endoplasmic reticulum (ER) membrane. How ER resident biogenesis factors coordinate membrane insertion, folding and assembly is not well understood. Here, we demonstrate that the ER membrane protein complex (EMC) insertase additionally acts as a chaperone to facilitate the assembly of heterotrimeric voltage-gated calcium channels (Ca). Using function-separating mutations and inhibitory nanobodies we show that nascent Ca channels are degraded prematurely when EMC's chaperone function is selectively perturbed. Blocking EMC's chaperone function strongly impaired Ca-dependent cardiomyocyte contraction. EMC engagement of the pore-forming Caα-subunit occurred co-translationally and required Caα's first transmembrane domain bundle to protrude from the nascent ribosome•Sec61•multipass translocon complex. Our findings establish a chaperone function for the EMC and reveal that biogenesis of multi-bundle membrane proteins requires a highly orchestrated, co-translational interplay between ER biogenesis factors.
History
DepositionJan 6, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ER membrane protein complex subunit 1
B: ER membrane protein complex subunit 2
C: ER membrane protein complex subunit 3
D: ER membrane protein complex subunit 4
E: Membrane magnesium transporter 1
F: ER membrane protein complex subunit 6
G: ER membrane protein complex subunit 7
H: ER membrane protein complex subunit 8
I: ER membrane protein complex subunit 10
K: Nanobody G9
L: Nanobody E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,27515
Polymers331,78111
Non-polymers1,4944
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ER membrane protein complex subunit ... , 8 types, 8 molecules ABCDFGHI

#1: Protein ER membrane protein complex subunit 1


Mass: 111886.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC1, KIAA0090, PSEC0263 / Production host: Homo sapiens (human) / References: UniProt: Q8N766
#2: Protein ER membrane protein complex subunit 2 / Tetratricopeptide repeat protein 35 / TPR repeat protein 35


Mass: 34882.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC2, KIAA0103, TTC35 / Production host: Homo sapiens (human) / References: UniProt: Q15006
#3: Protein ER membrane protein complex subunit 3 / Transmembrane protein 111


Mass: 29981.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC3, TMEM111 / Production host: Homo sapiens (human) / References: UniProt: Q9P0I2
#4: Protein ER membrane protein complex subunit 4 / Cell proliferation-inducing gene 17 protein / Transmembrane protein 85


Mass: 20104.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC4, TMEM85, HSPC184, PIG17 / Production host: Homo sapiens (human) / References: UniProt: Q5J8M3
#6: Protein ER membrane protein complex subunit 6 / Transmembrane protein 93


Mass: 12029.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC6, TMEM93 / Production host: Homo sapiens (human) / References: UniProt: Q9BV81
#7: Protein ER membrane protein complex subunit 7


Mass: 26501.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC7, C11orf3, C15orf24, HT022, UNQ905/PRO1926 / Production host: Homo sapiens (human) / References: UniProt: Q9NPA0
#8: Protein ER membrane protein complex subunit 8 / Neighbor of COX4 / Protein FAM158B


Mass: 23807.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC8, C16orf2, C16orf4, COX4AL, COX4NB, FAM158B, NOC4 / Production host: Homo sapiens (human) / References: UniProt: O43402
#9: Protein ER membrane protein complex subunit 10 / Hematopoietic signal peptide-containing membrane domain-containing protein 1


Mass: 27375.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC10, C19orf63, HSM1, INM02, UNQ764/PRO1556 / Production host: Homo sapiens (human) / References: UniProt: Q5UCC4

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Protein , 1 types, 1 molecules E

#5: Protein Membrane magnesium transporter 1 / ER membrane protein complex subunit 5 / Transmembrane protein 32


Mass: 14706.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMGT1, EMC5, TMEM32 / Production host: Homo sapiens (human) / References: UniProt: Q8N4V1

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Antibody , 2 types, 2 molecules KL

#10: Antibody Nanobody G9


Mass: 16805.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#11: Antibody Nanobody E2


Mass: 13699.886 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Sugars , 2 types, 4 molecules

#12: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#13: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of the human ER membrane protein complex (EMC) with Nanobodies E2 and G9
Type: COMPLEX / Entity ID: #1-#11 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.33121509 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human) / Cellular location: Endoplasmic reticulum
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5 / Details: pH 7.5 adjusted with KOH ( potassium hydroxide).
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM((4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)C8H18N2O4S1
2200 mMSodium ChlorideNaCl1
32 mMMagnesium AcetateMgAc1
41 mMDithiothreitolDTT1
50.05 wt/VolGlyco-diosgeninGDN1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Pelco easiglow / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5.79 sec. / Electron dose: 54.23 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPU3.8.1.7603image acquisition
4cryoSPARCCTF correction
7Coot0.9.8.96model fitting
8UCSF ChimeraX1.7model fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
14PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43012 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeInitial refinement model-IDSource nameTypeChain-IDDetails
18s9s

8s9s

8s9s1PDBexperimental model
2AlphaFoldin silico modelKnanobody
3AlphaFoldin silico modelLnanobody
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 185.92 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002421021
ELECTRON MICROSCOPYf_angle_d0.550328495
ELECTRON MICROSCOPYf_chiral_restr0.04153194
ELECTRON MICROSCOPYf_plane_restr0.00343636
ELECTRON MICROSCOPYf_dihedral_angle_d3.88352968

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